synthetic biology open language visual (sbol visual) version 2(p. fontanarrosa) vishwesh kulkarni:...

Hasan Baig, Pedro Fontanarrosa, Vishwesh Kulkarni, James McLaughlin,Prashant Vaidyanathan, Bryan Bartley, Swapnil Bhatia, Shyam Bhakta,Michael Bissell, Kevin Clancy, Robert Sidney Cox, Angel Goñi Moreno,Thomas Gorochowski, Raik Grunberg, Augustin Luna, Curtis Madsen, Goksel Misirli,Tramy Nguyen, Nicolas Le Novere, Zachary Palchick, Matthew Pocock,Nicholas Roehner, Herbert Sauro, James Scott-Brown, John T. Sexton, Guy-Bart Stan,Jeffrey J. Tabor, Marta Vazquez Vilar, Christopher A. Voigt, Anil Wipat, David Zong,Zach Zundel, Jacob Beal and Chris Myers*

Synthetic biology open language visual(SBOL visual) version 2.2https://doi.org/10.1515/jib-2020-0014Received March 30, 2020; accepted April 16, 2020; published online June 10, 2020

Abstract: People who are engineering biological organisms often find it useful to communicate in diagrams,both about the structure of the nucleic acid sequences that they are engineering and about the functionalrelationships between sequence features and othermolecular species. Some typical practices and conventionshave begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOLVisual) has beendeveloped as a standard for organizing and systematizing such conventions in order to produce a coherentlanguage for expressing the structure and function of genetic designs. This document details version 2.2 ofSBOL Visual, which builds on the prior SBOL Visual 2.1 in several ways. First, the grounding of molecularspecies glyphs is changed from BioPAX to SBO, aligning with the use of SBO terms for interaction glyphs.Second, new glyphs are added for proteins, introns, and polypeptide regions (e. g., protein domains), the prior

*Corresponding author: Chris Myers, University of Utah, Salt Lake City, USA, E-mail: [email protected] Baig: University of Connecticut, Storrs, USAPedro Fontanarrosa and Zach Zundel: University of Utah, Salt Lake City, USA. https://orcid.org/0000-0002-0535-2684(P. Fontanarrosa)Vishwesh Kulkarni: University of Warwick, Coventry, UKJames McLaughlin, Angel Goñi Moreno and Anil Wipat: Newcastle University, Newcastle upon Tyne, UKPrashant Vaidyanathan: Microsoft Research, Cambridge, UKBryan Bartley, Tramy Nguyen, Nicholas Roehner and Jacob Beal: Raytheon BBN Technologies, Cambridge, USA. https://orcid.org/0000-0002-1663-5102 (J. Beal)Swapnil Bhatia and Curtis Madsen: Boston University, Boston, USAShyamBhakta, John T. Sexton, Jeffrey J. Tabor and David Zong: Rice University, Houston, USA. https://orcid.org/0000-0002-8157-4780 (D. Zong)Michael Bissell: Shipyard Toolchains LLC, Emeryville, USAKevin Clancy: Thermo Fisher Scientific, San Diego, USARobert Sidney Cox: Kobe University, Kobe, JapanThomas Gorochowski: University of Bristol, Bristol, UKRaik Grunberg: KAUST, Thuwal, Saudi Arabia.Augustin Luna: Harvard Medical School, Boston, USAGoksel Misirli: Keele University, Keele, UKNicolas Le Novere: Babraham Institute, Cambridge, UKZachary Palchick: Zymergen, Emeryville, USAMatthew Pocock: Turing Ate My Hamster, Ltd., Newcastle, UKHerbert Sauro: University of Washington, Seattle, USAJames Scott-Brown: University of Oxford, Oxford, UKGuy-Bart Stan: Imperial College, London, UKMarta Vazquez Vilar: Universitat Politecnica de Valencia, Valencia, SpainChristopher A. Voigt: MIT, Cambridge, USA

Journal of Integrative Bioinformatics 2020; 17(2–3): 20200014

Open Access. © 2020 Hasan Baig et al., published by De Gruyter. This work is licensed under the Creative Commons Attribution4.0 Public License.

https://doi.org/10.1515/jib-2020-0014

mailto:[email protected]

https://orcid.org/0000-0002-0535-2684

https://orcid.org/0000-0002-0535-2684

https://orcid.org/0000-0002-1663-5102

https://orcid.org/0000-0002-1663-5102

https://orcid.org/0000-0002-8157-4780

https://orcid.org/0000-0002-8157-4780

recommended macromolecule glyph is deprecated in favor of its alternative, and small polygons are intro-duced as alternative glyphs for simple chemicals.

Keywords: diagrams; SBOL visual; standards.

2 H. Baig et al.: SBOL Visual 2.2

Journal of Integrative Bioinformatics, XX(X):XXX, XXXX http://journal.imbio.de/

Synthetic Biology Open Language Visual (SBOL Visual)Version 2.2

Hasan Baig1, Pedro Fontanarossa2, Vishwesh Kulkarni3, James McLaughlin4, PrasantVaidyanathan5, Bryan Bartley6, Swapnil Bhatia7, Shyam Bhakta8, Mike Bissell9, KevinClancy10, Robert Sidney Cox11, Angel Goni Moreno4, Thomas Gorochowski12, Raik

Grunberg13, Augustin Luna14, Curtis Madsen7, Goksel Misirli15, Tramy Nguyen6,Nicolas Le Novere16, Zachary Palchick17, Matthew Pocock18, Nicholas Roehner6,

Herbert Sauro19, James Scott-Brown20, John T. Sexton8, Guy-Bart Stan21, Jeffrey J.Tabor8, Marta Vazquez Vilar22, Christopher A. Voigt23, Anil Wipat4, David Zong8, Zach

Zundel2, Jacob Beal6, Chris Myers2*

1University of Connecticut, USA

2University of Utah, USA

3University of Warwick, USA

4Newcastle University, UK

5Microsoft Research, UK

6Raytheon BBN Technologies, USA

7Boston University, USA

8Rice University, USA

9Shipyard Toolchains LLC, USA

10Thermo Fisher Scientific, USA

11Kobe University, Japan

12University of Bristol, UK

13KAUST, Saudi Arabia

14Harvard Medical School, USA

15Keele University, UK*Correspondence should be addressed to: [email protected]

doi:10.2390/biecoll-jib-XXXX-XXX 1

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Journal of Integrative Bioinformatics, XX(X):XXX, XXXX http://journal.imbio.de/

16Babraham Institute, UK

17Zymergen, USA

18Turing Ate My Hamster, Ltd., UK

19University of Washington, USA

20University of Oxford, UK

21Imperial College, UK

22Universitat Politecnica de Valencia, Spain

23MIT, USA

Summary

People who are engineering biological organisms often find it useful to communicate in di-agrams, both about the structure of the nucleic acid sequences that they are engineering andabout the functional relationships between sequence features and other molecular species.Some typical practices and conventions have begun to emerge for such diagrams. The Syn-thetic Biology Open Language Visual (SBOL Visual) has been developed as a standard fororganizing and systematizing such conventions in order to produce a coherent language forexpressing the structure and function of genetic designs. This document details version2.2 of SBOL Visual, which builds on the prior SBOL Visual 2.1 in several ways. First,the grounding of molecular species glyphs is changed from BioPAX to SBO, aligning withthe use of SBO terms for interaction glyphs. Second, new glyphs are added for proteins,introns, and polypeptide regions (e.g., protein domains), the prior recommended macro-molecule glyph is deprecated in favor of its alternative, and small polygons are introducedas alternative glyphs for simple chemicals.

This document does not contain technology or technical data controlled under either the U.S.International Traffic in Arms Regulations or the U.S. Export Administration Regulations.

Keywords: SBOL Visual; Standards; Diagrams

doi:10.2390/biecoll-jib-XXXX-XXX 2

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http://journal.imbio.de/

Synthetic Biology OpenLanguage Visual (SBOL Visual) Version 2.2

Editors:Hasan Baig University of Connecticut, USAPedro Fontanarrosa University of Utah, USAVishwesh Kulkarni University of Warwick, UKJames McLaughlin Newcastle University, UKPrasant Vaidyanathan Microsoft Research, UK

[email protected]:

Chris Myers University of Utah, USAAdditional authors, by last name:

Bryan Bartley Raytheon BBN Technologies, USAJacob Beal Raytheon BBN Technologies, USASwapnil Bhatia Boston University, USAShyam Bhakta Rice University, USAMichael Bissell Shipyard Toolchains LLC, USAKevin Clancy Thermo Fisher Scientific, USARobert Sidney Cox Kobe University, JapanAngel Goni Moreno Newcastle University, UKThomas Gorochowski University of Bristol, UKRaik Grunberg KAUST, Saudi ArabiaAugustin Luna Harvard Medical School, USACurtis Madsen Sandia National Laboratories, USAGoksel Misirli Keele University, UKTramy Nguyen University of Utah, USANicolas Le Novere Babraham Institute, UKZachary Palchick Zymergen, USAMatthew Pocock Turing Ate My Hamster, Ltd., UKNicholas Roehner Raytheon BBN Technologies, USAHerbert Sauro University of Washington, USAJames Scott-Brown University of Oxford, UKJohn T. Sexton Rice University, USAGuy-Bart Stan Imperial College, UKJeffrey J. Tabor Rice University, USAMarta Vazquez Vilar Universitat Politecnica de Valencia, SpainChris Voigt MIT, USAAnil Wipat Newcastle University, UKDavid Zong Rice University, USAZach Zundel University of Utah, USA

Version 2.2

March, 2020

Copyright (C) all authors listed on the front page of this document.

This work is made available under the Creative Commons Attribution 4.0 International Public License.

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Contents1 Purpose 3

1.1 Relation to Data Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 Relation to other Standards 33 SBOL Specification Vocabulary 4

3.1 Term Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43.2 SBOL Class Names . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

4 SBOL Glyphs 64.1 Requirements for Glyphs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74.2 Reserved Visual Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84.3 Extending the Set of Glyphs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

5 SBOL Visual Diagram Language 95.1 Nucleic Acid Backbone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95.2 Nucleic Acid Sequence Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105.3 Molecular Species . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135.4 Interaction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145.5 Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155.6 Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175.7 Annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175.8 Criteria for Compliance with SBOL Visual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

A SBOL Visual Glyphs 19A.1 Sequence Feature Glyphs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19A.2 Molecular Species Glyphs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58A.3 Interaction Glyphs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67A.4 Interaction Node Glyphs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

B Examples 77C Relationship to SBOL Visual 1.0 80References 81

Page 2 of 81

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1 Purpose 1

People who engineer biological organisms often find it useful to draw diagrams in order to communicate both the 2

structure of the nucleic acid sequences that they are engineering and the functional relationships between sequence 3

features and other molecular species. Some typical practices and conventions have begun to emerge for such 4

diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language 5

for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple 6

and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, 7

and styled—in particular, it should be readily possible to create diagrams either by hand or using a wide variety of 8

software programs. Finally, means are provided for extending the language with new and custom diagram elements, 9

and for adoption of useful new elements into the language. 10

1.1 Relation to Data Models 11

In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with 12

well-defined semantics. In particular, glyphs in SBOL Visual are defined in terms of their relation to the SBOL 2 13

data model (as defined in BBF RFC 112) and terms in the Sequence Ontology (Eilbeck et al., 2005) and the Systems 14

Biology Ontology (Courtot et al., 2011). 15

SBOL Visual is not intended to represent designs at the same level of detail as these data models. Effective visual 16

diagrams are necessarily more abstract, focusing only on those aspects of a system that are the subject of the 17

communication. Nevertheless, we take as a principle that it should be possible to transform any SBOL Visual 18

diagram into an equivalent (if highly abstract) SBOL 2 data representation. Likewise, we require that SBOL Visual 19

should be able to represent all of the significant structural or functional relationships in any GenBank or SBOL data 20

representation. 21

2 Relation to other Standards 22

SBOL Visual 2.2 replaces SBOL Visual 2.1. Substantive differences between SBOL Visual 2.2 and SBOL Visual 2.1 are 23

marked with change bars identifying the version in which the new material was introduced. 24

SBOL Visual 2.2 also implicitly supersedes the previously replaced BBF RFC 115 (SBOL Visual 2.0), as well as BBF 25

RFC 93 and BBF RFC 16 (prior versions of SBOL Visual). 26

Every glyph in SBOL Visual 2.2 corresponds to an element of the SBOL 2.3 data model. SBOL Visual 2.2 also defines 27

many terms by reference to SBOL 2.3, or by reference to the Sequence Ontology (Eilbeck et al., 2005) or the Systems 28

Biology Ontology (Courtot et al., 2011). 29

SBOL Visual is intended to be compatible with the Systems Biology Graphical Notation Activity Flow Language 30

(SBGN AF) (Le Novère et al., 2009), and species and interaction glyphs have been imported from that language (see: 31

Appendix A.2 and Appendix A.3). Some aspects are also imported from the Systems Biology Graphical Notation 32

Process Description Language (SBGN PD). 33

Section Contents Page 3 of 81

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3 SBOL Specification Vocabulary 1

3.1 Term Conventions 2

This document indicates requirement levels using the controlled vocabulary specified in IETF RFC 2119 and 3

reiterated in BBF RFC 0. In particular, the key words "MUST", "MUST NOT", "REQUIRED", "SHALL", "SHALL NOT", 4

"SHOULD", "SHOULD NOT", "RECOMMENDED", "MAY", and "OPTIONAL" in this document are to be interpreted 5

as described in RFC 2119: 6

■ The words "MUST", "REQUIRED", or "SHALL" mean that the item is an absolute requirement of the specifica- 7

tion. 8

■ The phrases "MUST NOT" or "SHALL NOT" mean that the item is an absolute prohibition of the specification. 9

■ The word "SHOULD" or the adjective "RECOMMENDED" mean that there might exist valid reasons in 10

particular circumstances to ignore a particular item, but the full implications need to be understood and 11

carefully weighed before choosing a different course. 12

■ The phrases "SHOULD NOT" or "NOT RECOMMENDED" mean that there might exist valid reasons in 13

particular circumstances when the particular behavior is acceptable or even useful, but the full implications 14

need to be understood and the case carefully weighed before implementing any behavior described with this 15

label. 16

■ The word "MAY" or the adjective "OPTIONAL" mean that an item is truly optional. 17

3.2 SBOL Class Names 18

The definition of SBOL Visual references several SBOL classes, which are defined as listed here. For full definitions 19

and explanations, see BBF RFC 112, describing the SBOL 2.1 data model. 20

ComponentDefinition: Describes the structure of designed entities, such as DNA, RNA, and proteins, as well as 21

other entities they interact with, such as small molecules or environmental properties. 22

■ Component: Pointer class. Incorporates a child ComponentDefinition by reference into exactly one par- 23

ent ComponentDefinition. Represents a specific occurrence or instance of an entity within the design of 24

a more complex entity. Because the same definition might appear in multiple designs or multiple times in 25

a single design, a single ComponentDefinition can have zero or more parent ComponentDefinitions, 26

and each such parent-child link requires its own, distinct Component. 27

■ Location: Specifies the base coordinates and orientation of a genetic feature on a DNA or RNA molecule 28

or a residue or site on another sequential macromolecule such as a protein. 29

■ SequenceAnnotation: Describes the Location of a notable sub-sequence found within the Sequence 30

of a ComponentDefinition. Can also link to and effectively position a child Component. 31

■ SequenceConstraint: Describes the relative spatial position and orientation of two Component objects 32

that are contained within the same ComponentDefinition. 33

ModuleDefinition: Describes a “system” design as a collection of biological components and their functional 34

relationships. 35

■ FunctionalComponent: Pointer class. Incorporates a child ComponentDefinition by reference into 36

exactly one parent ModuleDefinition. Represents a specific occurrence or instance of an entity within 37

the design of a system. Because the same definition might appear in multiple designs or multiple times 38

in a single design, a single ComponentDefinition can have zero or more parent ModuleDefinitions, 39

and each such parent-child link requires its own, distinct FunctionalComponent. 40


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Section 3. SBOL Specification Vocabulary

■ Interaction: Describes a functional relationship between biological entities, such as regulatory activa- 1

tion or repression, or a biological process such as transcription or translation. 2

2.1.0 ■ MapsTo: When a design (ComponentDefinition or ModuleDefinition) includes another design as a 3

sub-design, the parent design might need to refer to a ComponentInstance (either a Component or 4

FunctionalComponent) in the sub-design. In this case, a MapsTo needs to be added to the instance for 5

the sub-design, and this MapsTo needs to link between the ComponentInstance in the sub-design and a 6

ComponentInstance in the parent design. 7

■ Module: Pointer class. Incorporates a child ModuleDefinition by reference into exactly one parent 8

ModuleDefinition. Represents a specific occurrence or instance of a subsystem within the design of 9

a larger system. Because the same definition in multiple designs or multiple times in a single design, 10

a single ModuleDefinition can have zero or more parent ModuleDefinitions, and each such parent- 11

child link requires its own, distinct Module. 12

■ Participation: Describes the role that a FunctionalComponent plays in an Interaction. For exam- 13

ple, a transcription factor might participate in an Interaction as a repressor or as an activator. 14


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4 SBOL Glyphs 1

A glyph is a visual symbol used to represent an element in an SBOL Visual diagram. All of the currently defined 2

glyphs are collected in Appendix A. This section explains how glyphs are specified and how to add new glyphs. 3

Each SBOL glyph is defined by association with ontology terms, and can be used to represent any diagram element 4

that is well-described by that term. Currently there are three classes of glyphs, each associated with a different 5

ontology and different class in the SBOL 2 data model: 6

■ Sequence Feature Glyphs describe features of nucleic acid sequences. They are associated with Sequence 7

Ontology terms. For the SBOL 2 data model, this is formally defined as any Componentwith a compatible term 8

within its associated roles, i.e., one that is equal to or a child of at least one term associated with the glyph. 9

■ Molecular Species Glyphs represent any class of molecule whose detailed structure is not being shown using 10

sequence feature glyphs. They are associated with Systems Biology Ontology terms. For the SBOL 2 data

2.2.0

11

model, this is formally defined as any FunctionalComponentwith a compatible term within its associated 12

types, i.e., one that is equal to or a child of at least one term associated with the glyph. 13

■ Interaction Glyphs are “arrows” indicating functional relationships between sequence features and/or molec- 14

ular species. They are associated with Systems Biology Ontology terms. For the SBOL 2 data model, this is 15

formally defined as any Interactionwith a compatible term within its types, i.e., one that is equal to or a 16

child of at least one term associated with the glyph, and with a compatible Participation at the head and 17

tail of the arrow. 18

More than one glyph may share the same definition: in this case, these glyphs form a family of variants, of which 19

precisely one MUST be designated as the RECOMMENDED glyph, which is to be used unless there are strong 20

reasons to prefer an alternative variant. 21

It will also frequently be the case that a diagram element could be represented by more than one glyph (e.g., a glyph 22

for a specific term and a glyph for a more general term). In such cases, it is RECOMMENDED that the most specific 23

applicable glyph be used. However, if upward branching in the relevant ontology means two applicable glyphs do

2.1.0

24

not have an ordered parent/child relation, then either MAY be used. 25

For example, a protein coding sequence (CDS) is a sequence feature that may be represented either using the CDS 26

glyph (Sequence Ontology term SO:0000316) or the Unspecified glyph (Sequence Ontology term SO:0000001). Since 27

SO:0000316 is contained by SO:0000001, the preferred glyph is CDS, rather than Unspecified. Likewise, a CDS may 28

be represented by either a pentagonal glyph or an arrow glyph, but the pentagon is the RECOMMENDED variant, 29

and so it is likewise preferred. Figure 1 illustrates this example. 30

SHOULD

gfp

MAY

gfp

SHOULDNOT

Figure 1: A biological design element such as a protein coding sequence (CDS) is best represented by the most specificRECOMMENDED glyph (middle), but can be represented by a less specific glyph such as Unspecified (left) or an approvedalternative glyph (right).


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Section 4. SBOL Glyphs

4.1 Requirements for Glyphs 1

A number of requirements are placed on all SBOL Visual glyphs in order to ensure both the clarity of diagrams and 2

the ease with which they can be constructed: 3

1. A glyph SHOULD have its meaning defined by associating the glyph with at least one ontology definition. 4

Definitions are RECOMMENDED to be from the Sequence Ontology for sequence feature glyphs, from 5

the Systems Biology Ontology for molecular species glyphs , and from the Systems Biology Ontology for

2.2.0

6

interaction glyphs. If no applicable terms are available in the preferred ontology, proposal of a new glyph 7

SHOULD be accompanied by a request to the ontology maintainers to add a term for the undefined entity. 8

2. A glyph SHOULD be relatively easy to sketch by hand (e.g., no high-complexity images or precise angles 9

required). 10

3. A glyph specification MUST indicate which portions of the glyph are the “interior” for purposes of color fill. 11

4. A glyph specification SHOULD show the glyph in its preferred relative scale with respect to other glyphs. 12

5. A glyph SHOULD be specified using only solid black lines (leaving color and style to be determined by the 13

user, as noted below). 14

6. A glyph SHOULD NOT be similar enough to be easily confused with any other glyph when written by hand, or 15

when scaled either vertically, horizontally, or both. 16

7. A glyph SHOULD NOT include text (note that associated labels are not part of the glyph). 17

In addition, some requirements apply only to certain classes of glyphs: 18

8. A sequence feature or molecular species glyph specification MUST include a rectangular bounding box 19

indicating its extent in space. 20

9. A sequence feature glyph specification MUST include exactly one horizontal rule for its RECOMMENDED 21

vertical alignment with the nucleic acid backbone. 22

10. A sequence feature glyph SHOULD be asymmetric on the horizontal axis. Vertical asymmetry is also preferred 23

when possible. 24

11. If a sequence feature glyph can represent components of highly variable size or structural complexity, the 25

glyph SHOULD be able to be scaled horizontally to indicate relative property value. 26

Figure 2 shows examples of compliant glyph specification. 27

Figure 2: Examples of glyph specification: this specification for the sequence feature glyphs for Promoter (left) andRibosome Entry Site (right) include the glyph outline, fill (grey center of Ribosome Entry Site), bounding box (dashed box),and recommended alignment with the nucleic acid backbone (dashed horizontal line), all at a preferred relative scale.


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Section 4. SBOL Glyphs

4.2 Reserved Visual Properties 1

SBOL Visual aims to allow as much flexibility and freedom as possible in how diagrams are organized, presented, 2

and styled. To this end, a number of aspects of presentation are generally reserved for the communication of other 3

types of information by the creator of a diagram. When using a glyph in a diagram, the following choices in glyph 4

presentation are thus explicitly intended to be alterable: 5

1. The lines of a glyph MAY be given any line thickness and style 6

2. The interior of a glyph MAY be given any fill color, as long as the choice of fill does not interfere with recognizing 7

the glyph. 8

3. The scale of glyphs are RECOMMENDED to be kept consistent with their specification and throughout 9

a diagram, but can be altered if desired, particularly to convey additional information (e.g., length of a 10

sequence). 11

4. Minor styling effects MAY be chosen (e.g., shadow, corner styling, other "font-level" customization) 12

Figure 3 shows some examples of acceptable style variation. 13

In certain special cases, the style of a glyph may be more constrained, but such cases are expected to be rare and 14

strongly motivated. 15

Figure 3: Examples of acceptable style variation for a Promoter glyph.

4.3 Extending the Set of Glyphs 16

The collection of SBOL Visual glyphs is not expected to provide complete coverage of all of the types of element that 17

people will wish to include in genetic diagrams, particularly given the ongoing evolution of synthetic biology as 18

an engineering discipline. As the need for new diagram elements or new practices of usage emerge, new glyphs or 19

glyph definitions are expected to be added to SBOL Visual. In particular, the following three classes of changes are 20

expected to occur regularly, and the SBOL development community will maintain clear processes for proposal and 21

adoption of changes of this type: 22

■ New glyphs, either representing a type of component that previously lacked a glyph or enabling a distinction 23

between types of components previously represented by the same glyph. 24

■ Additional glyph variants, accompanied by compelling use cases that cannot be adequately addressed by the 25

existing glyph variants. 26

■ Additional definitions for a glyph, capturing an alternate meaning that is useful to humans but existing within 27

a disjoint branch of the relevant ontology. 28

In order to support the coherent extension of SBOL Visual, whenever a diagram creator uses a glyph not found in 29

Appendix A, the creator SHOULD submit it to be considered for inclusion in an updated version of the standard 30

following the processes for adding new glyphs found on the community website at http://sbolstandard.org 31


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5 SBOL Visual Diagram Language 1

An SBOL Visual diagram represents information about the structure of a nucleic acid design and its associated 2

molecular species and interactions. If desired, an SBOL Visual diagram may also be associated with a machine- 3

interpretable model (e.g., in SBOL, GenBank, or SBML format). In this document we describe the association 4

for the SBOL 2 data model, which provides a formal semantic grounding for all elements of an SBOL Visual 5

diagram, but equivalent associations may be made between diagram elements and other models. In terms of 6

the SBOL 2 data model, the description of a nucleic acid design is formally defined as a representation of a 7

ComponentDefinitionwith a nucleic acid type, the Component and SequenceAnnotation objects describing the 8

features and sub-structure of the design, and SequenceConstraint information on the relative positions of such 9

elements. The description of interactions between some number of nucleic acid designs and other molecular species 10

is formally defined as a representation of a ModuleDefinition, the FunctionalComponent objects describing the 11

nucleic acid designs and other molecular species, and the Interaction and Participation objects describing 12

their functional relationships. 13

Featureon+Strand

Featureon- Strand

SequenceFeature

NucleicAcidConstruct

Annotation

MolecularSpecies

MolecularSpecies

Interaction

Interaction

Interaction

Figure 4: Generic syntax of SBOL Visual 2: a diagram for a nucleic acid construct is based around a backbone line, itsstructure specified by the sequence of attached sequence feature glyphs. Strand can optionally be indicated by placing aglyph above or below the backbone. Other molecular species are indicated by glyphs not in contact with any backbone.Interactions are directed edges connecting sequence feature or molecular species glyphs. Any of these objects may havean associated label showing its name, and the diagram may further include any form of other annotations, including othertypes of text.

Specifically, an SBOL Visual diagram consists of the classes of objects illustrated in Figure 4. Figure 5 shows an 14

example of such a diagram, in a typical usage. Full details of this specification are provided in the remainder of this 15

section. 16

5.1 Nucleic Acid Backbone 17

A diagram for a nucleic acid construct is based around a single or double line, representing the nucleic acid 18

backbone. Information about features of the construct can then be represented by attaching nucleic acid glyphs 19

to the backbone, as defined below in Section 5.2. In terms of the SBOL 2 data model, the backbone represents 20

a ComponentDefinition with a nucleic acid type (e.g., DNA, RNA), and the features represent Component and 21

SequenceAnnotationmembers of the ComponentDefinition. 22

1. Lines in some cases indicate strand count. A double-stranded region of the nucleic acid construct MAY use 23

either a single or double line for the backbone. A single-stranded region of the nucleic acid construct MUST 24

use a single line to indicate the backbone. When single and double lines are mixed within a single diagram, 25

the single lines always indicate single-stranded regions. Examples are provided in Figure 6. 26


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Section 5. SBOL Visual Diagram Language

gfp tetR

NucleicAcidBackbone

SequenceFeatureGlyphs

ReverseComplementNucleicAcidComponentGlyphs

pTet

Labels Interactions

GFP

MolecularSpeciesGlyph

Figure 5: Example illustrating the elements of an SBOL Visual 2 diagram, with nucleic acid sequence features on theforward and reverse strand of a backbone, other molecular species, and interactions between elements; the grey labels andindicator lines are annotations.

(a) Single- or double-strand backbone (b) Double-strand backbone (c) Double-strand backbone with single-strand overhangs

Figure 6: Examples of indicating strand count in nucleic acid backbones.

2. A nucleic acid backbone SHOULD be horizontal in orientation, but MAY use non-horizontal structure to 1

indicate important physical attributes (e.g., a closed loop to indicate a cyclic plasmid or more complex shapes 2

for DNA nanotech structures). Examples are provided in Figure 7. 3

2.1.03. As a special case of non-horizontal backbone structure, certain stylized backbone shapes are used as se- 4

quence feature glyphs to indicate the genomic context of a sequence. These glyphs SHOULD be used as a 5

matched pair, indicating the bounds of the context region. It is further RECOMMENDED that each glyph be 6

concatenated with an Omitted Detail glyph to explicitly indicate that some surrounding context is not being 7

shown. Examples are provided in Figure 8. 8

4. A nucleic acid backbone SHOULD have at least one associated feature glyph (else no structural information is 9

being provided). 10

5.2 Nucleic Acid Sequence Features 11

A glyph in contact with a nucleic acid backbone indicates a feature of the nucleic acid sequence. In terms of the 12

SBOL 2 data model, this is either a SequenceFeature or a Component with a nucleic acid type that is contained 13

within the ComponentDefinition associated with that nucleic acid backbone. The Componentmay be contained 14

either directly, as one of the components of the ComponentDefinition, or recursively through a sequence of such 15

containments. 16

1. Every feature glyph MUST have its bounding box in contact with the backbone for the nucleic acid construct 17

it describes. The placement of the glyph SHOULD follow the recommendation for backbone alignment in the 18

glyph specification. Examples are provided in Figure 9. 19

2. The horizontal orientation of a glyph can be used to indicate the strand alignment of a feature, as shown in 20


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RECOMMENDED

SHOULD NOT

SHOULD NOT

MAY

MAY

Figure 7: Recommended, acceptable, and problematic examples of nucleic backbone orientation.

... ...

(a) Functional unit on a circular plasmid

... ...

(b) Functional unit integrated at a chromosomal locus

... ... ...amyE ganA

(c) Two functional units on the same chromosome but different loci.

Figure 8: Examples of RECOMMENDED indication of genomic context.

Figure 10. Any glyphs for a feature associated with the inline strand SHOULD be placed in the prototypical 1

orientation given by the specification, while any glyph that is associated with the reverse complement strand 2

SHOULD be inverted vertically and horizontally (i.e., rotated 180 degrees). Reverse complement MAY also be 3


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(a) MUST (b) MUST NOT

Figure 9: Examples of correct and incorrect association of glyphs with a nucleic acid backbone.

indicated by horizontal-only inversion. Finally, a glyph inverted only vertically still indicates inline strand, but 1

it is RECOMMENDED NOT to use this orientation. Orientation SHOULD be used consistently throughout a 2

diagram, rather than mixing conventions. Examples are provided in Figure 11. 3

RECOMMENDED

RECOMMENDED

MAY

SHOULDNOT

inline

reversereverse

inline

Figure 10: Use of glyph orientation to indicate inline vs. reverse complement direction.

+ -+ ++-- -

Figure 11: Example construct incorporating both inline (+) and reverse complement (-) features.

3. Nucleic acid features in a sequential relationship SHOULD be drawn from 5’ left to 3’ right on the inline 4

strand and from 5’ right to 3’ left on the reverse complement strand. In terms of the SBOL 2 data model, this 5

indicates a SequenceConstraint on the relative ordering of two features. 6

4. Nucleic acid features that do not overlap in their locations SHOULD NOT have glyphs whose bounding boxes 7

overlap. An example is provided in Figure 12.

Figure 12: Example of incorrect glyph overlap: promoter (arrow) does not overlap in sequence with the ribosome entry siteand CDS, so SHOULD NOT overlap visually with them.


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5. Nucleic acid features that overlap in their locations SHOULD have glyphs whose bounding boxes overlap. 1

Overlap size MAY be used to indicate relative position. Examples are provided in Figure 13. 2

(a) Restriction site in a CDS (b) 3’-side operator in a promoter (c) 5’-side operator in a promoter

Figure 13: Examples where glyphs SHOULD overlap, but might not if it is more clear, e.g., with an operator site locatedwithin the 5’ portion of a promoter.

6. A nucleic acid feature SHOULD be represented using a glyph defined in Appendix A.1. In this case, the feature 3

MUST be contained within at least one of the glyph’s associated terms. In terms of the SBOL 2 data model, 4

this means the glyph is equal to or a parent of at least one of the roles for the Component or its associated 5

ComponentDefinition. Moreover, the glyph used SHOULD be the RECOMMENDED variant of the most 6

specific applicable glyph. Note that novel glyphs not defined in Appendix A.1 MAY be used, but SHOULD be 7

proposed for adoption as described in Section 4.3. Examples are provided in Figure 14.

(a) SHOULD (b) MAY

? ? ? ?

(c) SHOULD NOT (d) MUST NOT

Figure 14: Examples of recommended, allowed, and forbidden representation of a ComponentDefinition comprising asequence of promoter, ribosome entry site, CDS, and terminator: (a) is RECOMMENDED because it uses the preferredvariant of the most specific defined glyphs, (b) is allowed because it uses some novel custom non-conflicting symbol,not matching any glyph defined in this document, to encode more specific information about the particular CDS, (c) isrecommended against because it uses less specific glyphs, and (d) is forbidden because it use a promoter symbol torepresent the terminator.

8

5.3 Molecular Species 9

A glyph that is not in contact with any backbone represents any class of molecule whose detailed structure is not 10

being shown using sequence feature glyphs. In other words, either not a nucleic acid (e.g., proteins, small molecules) 11

or else an “uninteresting” nucleic acid (e.g., showing a transcribed mRNA, but not the features of its sequence). 12

In terms of the SBOL 2 data model, this is a FunctionalComponent that is contained within a ModuleDefinition 13

implicit in the diagram. 14

1. A molecular species glyph MUST NOT contact any nucleic acid backbone with any part of its bounding box. 15

2. A molecular species SHOULD be represented using a glyph defined in Appendix A.2. In this case, the species 16

MUST be contained within at least one of the glyph’s associated terms. In terms of the SBOL 2 data model, this 17

means the glyph is equal to or a parent of at least one of the types for the associated ComponentDefinition. 18

Moreover, the glyph used SHOULD be the RECOMMENDED variant of the most specific applicable glyph. 19


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Note that novel glyphs not defined in Appendix A.2 MAY be used, but SHOULD be proposed for adoption as 1

described in Section 4.3. 2

5.4 Interaction 3

A directed edge “arrow” attached to one or more glyphs indicates a functional interaction involving those elements. 4

The roles of the elements is indicated by their position at the head or tail of the edge. In terms of the SBOL 2 data 5

model, this is an Interaction, with either one or two Participation relationships, their role set by position at 6

the head or tail of the edge. An example is provided in Figure 15. 7

Figure 15: Example of an interaction indicating a promoter stimulated by the CDS that it regulates.

1. Two interaction edges SHOULD NOT cross one another. When edges cross, they MUST indicate the distinction 8

between arrows with a crossover pattern, in which one edge “diverts” at the intersection (see Figure 16). 9

Examples are provided in Figure 17. 10

Figure 16: Examples of Interaction crossover patterns.

(a) SHOULD (b) MAY (c) MUST NOT

Figure 17: Examples of recommended, allowed, and forbidden relationships between two interactions in a mutual repressionsystem: (a) non-crossing is recommended, (b) using a crossover pattern is allowed, but (c) crossing without a crossoverpattern is forbidden, since the relationship between the two edges is ambiguous.

2. An interaction SHOULD be represented using a glyph defined in Appendix A.3. In this case, the interaction 11

type MUST be contained within at least one of the glyph’s associated terms. In terms of the SBOL 2 data 12

model, this means the glyph is equal to or a parent of at least one of the types for the Interaction, and that 13

each associated Participation object has a role compatible with its position on the head or tail of the edge. 14

Moreover, the glyph used SHOULD be the RECOMMENDED variant of the most specific applicable glyph. 15

Note that novel glyphs not defined in Appendix A.3 MAY be used, but SHOULD be proposed for adoption as 16

described in Section 4.3. 17

2.1.0


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3. An edge may have multiple heads or multiple tails. In this case, a split or join in an edge represents either 1

multiple participants with the same role (e.g., a transcription factor repressing two instances of a promoter) 2

or a biochemical process (e.g., association of an inducible protein and a small molecule to form an active 3

complex). An edge with multiple heads MUST use the same glyph for each head. An edge that splits or joins 4

with no glyph at the junction represents multiple participants with the same role. A glyph at the point where 5

an edge splits or joins represents a biochemical process, i.e., an additional Interactionwith type and roles 6

set by the process glyph. Examples are provided in Figure 18. 7

(a) MAY

(b) MAY (c) MAY (d) MAY

(e) MAY

(f) MUST NOT

Figure 18: Examples of use of multi-head and multi-tail arrows: (a) Repression from multiple independent sources, (b)repressor with multiple targets, (c) association of gRNA and Cas9 into an active CRISPR complex and (d) the dissociationof that complex, and (e) composite edges representing two interactions: CRISPR complex formation with Cas9 from twosources, which then represses a promoter. (f) Multi-head interactions, however, MUST NOT use different glyphs for differentheads.

4. A biochemical process represented by a glyph at an edge junction SHOULD be represented using a glyph 8

defined in Appendix A.4. In this case, the interaction type MUST be contained within at least one of the glyph’s 9

associated terms. In terms of the SBOL 2 data model, this means the glyph is equal to or a parent of at least one 10

of the types for the Interaction, and that each associated Participation object has a role compatible 11

with its position on the head or tail of the edge. Moreover, the glyph used SHOULD be the RECOMMENDED 12

variant of the most specific applicable glyph. Note that novel glyphs not defined in Appendix A.4 MAY be used, 13

but SHOULD be proposed for adoption as described in Section 4.3. 14

2.1.0

5.5 Modules 15

A module within a system MAY be represented by a visual boundary in the form of closed polygon or closed curve. 16

Everything inside of the boundary is part of the module, and everything outside of the boundary is not part of the 17

module; only certain diagram elements are allowed to cross a boundary, as defined below. In terms of the SBOL 2 18

data model, the line represents a Module included within the ModuleDefinition represented by the surrounding 19

diagram, and boundary-crossing elements define MapsTo relationships. Note that the internals of a module need 20


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not be shown: some details can be omitted or a module can even be a “black box” with no internal structure at all 1

being shown. 2

1. The boundary of module SHOULD should be a rectangle or rounded rectangle. Boundary sides SHOULD be 3

oriented vertically and horizontally. It is RECOMMENDED that a module be made visually distinct by making 4

it larger than other glyphs and with a different line style. Examples are provided in Figure 19. 5

(a) SHOULD

ProductionModule

(b) SHOULD

(c) SHOULD NOT (d) SHOULD NOT

Figure 19: Examples of recommended and problematic module boundaries: (a) two modules with visually distinctrectangular borders, (b) shows the same modules but with rounded rectangles and the second being a “black box” modulewith no internal structure shown, (c) shows modules with non-rectilinear borders, and (d) shows a black-box module that isnot visually distinct from a sequence feature glyph.

2. An undirected edge (i.e., having no “arrow head”) that crosses the boundary of a module represents a mapping 6

associating the diagram elements that it links. Glyphs associated by a mapping MUST either be sequence 7

features, molecular species, or module ports (see below), and must be of compatible types. In terms of 8

the SBOL 2 data model, the line represents a MapsTo relationship between a FunctionalComponent in the 9

ModuleDefinition and another FunctionalComponent in the definition of the Module. Mapping edges 10

SHOULD be made visually distinct from other lines in the same diagram, and it is RECOMMENDED that this 11

distinction be made using dashed lines to represent mapping edges. Examples are provided in Figure 20. 12

(a) MAY (b) SHOULD NOT

(c) MUST NOT

Figure 20: Examples of recommended and problematic mappings: (a) mapping showing that the promoter inside themodule on the left is also used in the construct on the right, (b) mapping is not visually distinct from nucleic acid backbone,(c) mapping cannot identify a promoter with a macromolecule species.

3. Glyphs for sequence features and molecular species MUST NOT intersect with the boundary of a module. A 13


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nucleic acid backbone MAY cross the boundary of a module. This represents an implicit mapping between 1

the region of the nucleic acid construct contained within the module and a compatible region of the larger 2

construct represented in the enclosing system. An interaction edge MAY cross the boundary of a module. This 3

represents an interaction in the enclosing system plus an implicit mapping between the component inside of 4

the module and a compatible instance in the enclosing system. Examples are provided in Figure 21. 5

(a) MUST NOT

(b) MAY (c) MAY

Figure 21: Examples of recommended and problematic boundary intersections: (a) sequence feature and molecularspecies glyphs MUST NOT intersect a module boundary, (b) implicit mapping from the promoter in the left module and theregulated elements in the right module to a nucleic acid construct ordering both into a complete functional unit, (c) implicitmapping from the CDS in the left module and the promoter in the right module to instances in the complete system in whichthe CDS inhibits the promoter (presumably by a repressor product).

4. Small rectangles MAY be drawn on the outside of the module boundary to represent input/output ports. In 6

terms of the SBOL 2 data model, each rectangle is associated with a FunctionalComponentwith a direction 7

property that is in, out, or inout. A port may be connected to an interaction edge head or tail to represent 8

interactions with its associated component. If both a port and a glyph for its associated component are 9

present in a diagram, then they MUST be visually connected, either explicitly by means of a mapping or 10

implicitly by an interaction that passes through the port rectangle. Likewise, mappings and interactions with 11

the associated component MUST NOT cross the boundary except through the port. A port SHOULD NOT 12

both have interactions both connecting to it and crossing the boundary across it. Examples are provided 13

in Figure 22. 14

5.6 Labels 15

The name of any object in a diagram is RECOMMENDED to be displayed as text within, adjacent to, or otherwise 16

clearly visually connected to the object’s associated glyph. In terms of the SBOL 2 data model, this is the name 17

property, and if no name is supplied then the displayIdMAY be used instead. Examples are provided in Figure 23. 18

5.7 Annotations 19

Other text or graphics may be included as annotations with no constraint on their syntax or semantics. 20

1. Annotations SHOULD NOT be displayed in a way that allows them to be confused with other SBOL Visual 21

elements. 22

2. Annotations SHOULD NOT be used to display information that can be displayed using other SBOL Visual 23

elements. 24


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TetR-Regulated Production

TetR

(a) MAY (b) MAY

(c) MAY (d) SHOULD NOT

(e) MUST NOT (f) MUST NOT

Figure 22: Examples of recommended and problematic module ports: (a) port on a black-box module, (b) ports connectedto module internals via mappings, (c) boundary-crossing interaction passing through a port, (d) diagrams SHOULD NOTmix mappings and interactions on a give port, (e) ports MUST NOT be disconnected from their associated glyphs, and (f) ifa port exists, interactions with that port MUST NOT cross the boundary at any other location.

pTetmCherry

B0015

Figure 23: Examples of labels on glyphs.

5.8 Criteria for Compliance with SBOL Visual 1

A diagram of a biological system is compliant with SBOL Visual if it complies with all MUST and MUST NOT 2

requirements as specified above. A diagram is compliant with SBOL Visual best practices if it also complies with all 3

RECOMMENDED, SHOULD, and SHOULD NOT statements as specified above. 4

Importantly, note that a non-SBOL glyph can be used in a compliant diagram when its definition is a subset or 5

superset of a definition that does have an SBOL Visual glyph. For example, a diagram that creates a new glyph for a 6

special type of promoter can be SBOL Visual compliant even though there is an SBOL Visual glyph for a general 7

promoter. 8

A piece of software or other system for producing diagrams is compliant with SBOL Visual under the following 9

conditions: 10

1. The system MUST be capable of producing diagrams that are compliant with SBOL Visual. 11

2. If the system can also produce diagrams that are not compliant with SBOL Visual, it MUST clearly distinguish 12

to the user between compliant and non-compliant usage and diagrams. 13


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A SBOL Visual Glyphs 1

The following pages present all current glyphs for SBOL Visual, organized by glyph families. Each entry lists: 2

■ Glyph family name 3

■ Associated ontology terms 4

■ Recommended and alternate glyphs 5

■ At least one example of when this glyph would be used 6

■ Any additional notes 7

A.1 Sequence Feature Glyphs 8

These glyphs represent features of nucleic acid sequences, and include a bounding box (grey dashed box) and a 9

recommended alignment to the nucleic acid backbone (grey dashed horizontal line). 10


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Aptamer

Associated SO term(s)

SO:0000031: Aptamer

Recommended Glyph and Alternates

The aptamer glyph is a cartoon diagram of a prototypical nucleic acid secondary structure for anaptamer:

Prototypical Example

theophylline aptamer

Notes

this section deliberately blank

Section A. SBOL Visual Glyphs

1


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Assembly Scar


SO:0001953


The assembly scar glyph is an "equal sign" image, the pattern produced by the union of a 5' stickyend and 3' sticky end glyph. The scar will cover the backbone, creating a visual break suggestingthe potential disruption associated with a scar:

With a double-stranded backbone:


Ligated sticky ends following BioBrick assembly.

Notes



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Blunt Restriction Site


SO:0001691


The blunt restriction site glyph is an image of two brackets facing away from one another to makea smooth-edged gap:


EcoRV restriction site

Notes



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CDS


SO:0000316


The coding sequence glyph is a "box" with one side bent out arrow-like to show direction:

Alternately, CDS may be represented as a block arrow:


α-Hemoglobin coding sequence

Notes



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Chromosomal Locus


SO:0000830 Chromosome Part


The glyph to indicate integration into a chromosome is an S-shaped curve of the backbone,suggesting something that might be part of a larger looping structure:


B. subtilis amyE locus

Notes

Complementary "left" and "right" versions of this glyph SHOULD be used together, flanking theregion whose genomic context is being described.

The Omitted Detail glyph SHOULD generally be contatenated to indicate that there is informationabout the chromosome not being represented.

Examples of RECOMMENDED usage:

A functional unit consisting of promoter, ribosome entry site, CDS, and terminator, allintegrated together into the chromosome:

Two functional units, one integrated into the amyE locus, another integrated into the ganAlocus:


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Circular Plasmid


SO:0002211 Circular Plasmid - A self replicating circular nucleic acid molecule that is distinct froma chromosome in the organism.


The glyph to indicate embedding in a plasmid is a turn of the backbone indicating its circularstructure:


E. coli p15A plasmid

Notes

Note that for SBOL data representations, circularity SHOULD also be indicated with a type ofSO:0000988.

Complementary "left" and "right" versions of this glyph SHOULD be used together, flanking theregion whose genomic context is being described.

The Omitted Detail glyph SHOULD generally be concatenated to indicate that there is informationabout the plasmid not being represented.

Example of RECOMMENDED usage: a plasmid containing a functional unit consisting of promoter,ribosome entry site, CDS, and terminator:


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Cleavage Site


SO:0001956 (Protease Site)

SO:0001977 (Ribonuclease Site)

SO:0001688 (Restriction Enzyme Cleavage Junction), SO:0001687 (Restriction Enzyme RecognitionSite)


Cleavage Site is a "stem-top" glyph for describing small sites. In this system:

the top glyph indicates the type of site (e.g., Cleavage Site)the stem glyph indicates whether the site affects DNA, RNA, or protein (respectively:straight, wavy, or looped)

The Cleavage Site top is an "X" suggesting slicing on top of a stem connecting to the backbone atthe point where cleavage will occur (in order: DNA, RNA, Protein):


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RNAse E site, BamHI

Notes

SO:0000061 (which was previously associated with Restriction Enzyme Recognition Site in SBOLVisual 1.0) is no longer associated with the DNA Cleavage glyph in SBOL Visual 2, as SO:0000061refers to the binding site and not the location of cleavage.

The Ribonuclease Site, Protease Site, and Restriction Enzyme Recognition Site glyphs from SBOLVisual 1.0 are now replaced by the Cleavage Site glyph with the appropriate stem.

Describing a Restriction Enzyme Cleavage Site with a vertical line glyph on a DNA backbone (asdone previously in SBOL Visual 1.0 via the Restriction Enzyme Recognition Site glyph) can persistin a SBOL Visual 2 diagram and still be considered compliant with SBOL Visual 2, where it is nowclassified as a Biopolymer Location (which is a superclass of cleavage sites). Thus, the BiopolymerLocation glyph from SBOL Visual 2.0 is backwards compatible with the Restriction EnzymeRecognition Site glyph from SBOL Visual 1.0.

The 5' Sticky Restriction Site, 3' Sticky Restriction Site, and Blunt Restriction Site glyphs remainunchanged, and are more specific children/derivatives of the DNA-Stem Cleavage-Top glyph.


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Composite


Composite does not have an associated SO term, as it merely links a base glyph (with its own SOterm) to a sub-diagram (comprising glyphs with their own associated SO terms).


The glyph for Composite is dashed "expanding lines" connecting any "base" glyph representing themore abstract composite (e.g., Omitted Detail, or Terminator, or Promoter) to a backbonediagramming the contents of the composite. Note the bounding box is indicating the location ofthe base glyph, and would scale with that glyph.


An "expression cassette" containing a ribosome entry site, coding sequence, and terminator.

In this case, the recommended "base" glyph would be Engineered Region.

Notes

An "abbreviated" representation of composite, simply indicating that more structure is available,can be made by using short lines and placing only an Omitted Detail glyph in the secondarybackbone. For example, here is an example of an abbreviated composite promoter:

and a composite with an Engineered Region of otherwise unspecified content:


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Engineered Region


SO:0000804 (Engineered Region)


Engineered Region is represented by a plain rectangle suggesting a blank slate to be written upon:


An "expression cassette" containing a ribosome entry site, coding sequence, and terminator.

Notes



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Insulator


SO:0000627


The insulator glyph is a box inside another box that isolates it from its environment:


RiboJ

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Intron


SO:0000188 (intron)


An intron is designated by a boundaries interrupting CDS, each side having a two-triangle "tornout" edges, suggesting removal from an enclosing coding sequence:


Example of a coding sequence with three domains: an N-tag (blue), C-tag (yellow), and internalregion (red) interrupted by an intron that includes a gRNA non-coding RNA sequence (green):

Notes



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Biopolymer Location


SO:0000699 (Junction, Boundary, Breakpoint)

SO:0001236 (Base)

SO:0001237 (Amino Acid)


Biopolymer Location is a "stem-top" glyph for describing small sites. In this system:

the top glyph indicates the type of site (e.g., Biopolymer Location)the stem glyph indicates whether the site affects DNA, RNA, or protein (respectively:straight, wavy, or looped)

The RECOMMENDED top for Biopolymer Location is a circle, reminiscent of a pin stuck into alocation (in order: DNA, RNA, Protein):


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An alternative is to have "nothing" for the top, just an extended version of the stem itself (in order:DNA, RNA, Protein):


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CRISPR-targeted insertion site, protease site, mutation site

Notes

Biopolymer Location is a general glyph for all zero- and one-length sequence features, includinginsertion and deletion sites and X-ase cut sites.

Note also that Biopolymer Location does not cover stability elements, since their length is typicallymultiple bases / amino acids.

Describing a Restriction Enzyme Cleavage Site with a vertical line glyph on a DNA backbone (asdone previously in SBOL Visual 1.0 via the Restriction Enzyme Recognition Site glyph) can persistin a SBOL Visual 2 diagram and still be considered compliant with SBOL Visual 2, where it is nowclassified as a Biopolymer Location (which is a superclass of cleavage sites). Thus, the BiopolymerLocation glyph from SBOL Visual 2.0 is backwards compatible with the Restriction EnzymeRecognition Site glyph from SBOL Visual 1.0.


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No Glyph Assigned


Any SO term that is not covered by any glyph besides the root Sequence Feature


When a part has no assigned glyph it is RECOMMENDED that a user provide their own glyph. Theuser is also encouraged to submit the new glyph for possible adoption into the SBOLv standard.

An alternative is brackets, suggesting information that needs to be filled in:

As a best practice, it is RECOMMENDED that the name of the term be put in between the brackets.


No Glyph Assigned is intended to be used for any Component that is not covered by other SBOLVisual glyphs.

For example, at present there is no glyph recommended for representing a transposon.

Notes

No Glyph Assigned is intended for constructs with a defined specific role that happens to not yetbe covered by available approved glyphs (other than the root "Sequence Feature"). It is more likelyto appear in machine-generated diagrams than in human-generated diagrams, since humans arelikely to invent and use their own glyph for the purpose.


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Non-Coding RNA Gene


SO:0001263: Non-Coding RNA Gene

SO:0000834: Mature Transcript Region


The non-coding RNA glyph is a rectangular box whose top is a single-stranded RNA "wiggle":


gRNA sequence for targeting a dCas9 repressor

Notes

This section left deliverately blank


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Omitted Detail


No SO term is associated with Omitted Detail, as it is indicating that something is not beingrepresented.


The Omitted Detail glyph is a break in the backbone with an ellipsis to indicate that material wouldnormally be in that location:


A diagram in which a sequence feature is not drawn.

Notes

This glyph actually places a "break" in the nucleic acid backbone.


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Operator / Binding Site


SO:0000057 Operator

SO:0000409 Binding Site


The operator glyph is an open "cup" suggesting a binding location:


Gal4 binding site in an activatable promoter.

Notes

This glyph puts a "dent" in the backbone line.


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Origin of Replication


SO:0000296


The origin of replication glyph is a circle suggesting the "bulge" opened in a piece of circular DNAwhen replication is beginning:


human herpesvirus-6 OOR

Notes

The label on an origin of replication glyph is RECOMMENDED as the location to label eitherspecifically the identity of the origin of replication or the name of the entire plasmid backbonemore generally.


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Origin of Transfer


SO:0000724: Origin of Transfer


The origin of transfer glyph is circular like origin of replication, but also includes an outboundarrow:


oriT

Notes

This section left deliberately blank


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Overhang Site


SO:0001932: 5' Overhang Site

SO:0001933: 3' Overhang Site


The 5' overhang site glyph is an image of a strand of DNA extended on the 5' edge of its forwardstrand, and the complementary 3' Overhang Site glyph is a reflection of the 5' Overhang Site (inorder: five-prime, three-prime):

With a double-stranded backbone (in order: five-prime double stranded, three-prime doublestranded):


EcoRI site after cleavage.

Notes


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PolyA Site


SO:0000553: polyA Site


The polyA site glyph is a sequence of As sitting atop the backbone:


polyA tail on mammalian coding sequence

Notes



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Polypeptide Region


SO:0000839 (polypeptide region)


A polypeptide region inside a coding sequence is indicated by insertion of triangular boundariesinside of the CDS, parallel to the 3' side of the CDS. This will produce chevron segments on the 3'side and a CDS shape on the 5' side:


degradation tag on a protein coding sequence

nuclear localization tag on a protein coding sequence

coding sequence for the membrane-crossing region of a protein

This glyph is intended to be used in composition or superposition with the glyph for the codingsequence of which the polypeptide regions are fragments: Example of a coding sequence withthree designated domains, an N-tag (blue), C-tag (yellow), and internal region (red):

Notes



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Primer Binding Site


SO:0005850


The primer binding site glyph is a line with a bent end suggesting a partially complementarystrand of nucleic acid attaching to the backbone:


seq-F

Notes



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Promoter Site


SO:0000167


The promoter glyph is a bent arrow pointing forward, suggesting the action of transcription fromits transcription start site:


The lacYZA promoter

Notes



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Ribosome Entry Site


SO:0000139: Ribosome Entry Site


The ribosome entry promoter glyph is a half-ovoid sitting on the backbone, suggesting anattached ribosome beginning transcription:


T7g10 ribosome binding site

Notes



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Signature


SO:0001978


The signature glyph is a box sitting atop the backbone with an X and line inside it, suggesting asignature on a form:


DNA Barcode

Notes



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Specific Recombination Site


SO:0000299: Specific Recombination Site


The specific recombination site glyph is a triangle, centered on the backbone, as has appeared in anumber of recombinase circuit papers:


flippase recognition target (FRT) site

Notes



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Stability Element


SO:0001955, SO:0001546 (Protein Stability Element)

SO:0001979 (RNA Stability Element)

No SO term is currently associated with DNA stability.


Stability Element is a "stem-top" glyph for describing small sites. In this system:

the top glyph indicates the type of site (e.g., Stability Element)the stem glyph indicates whether the site affects DNA, RNA, or protein (respectively:straight, wavy, or looped)

The top for a Stability Element is a pentagon suggesting the shape of a shield, on top of a stemconnecting to the backbone at the point where the stability element is located (in order: DNA,RNA, Protein):


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PEST tag, 3ʼ Hairpin

Notes

RNA Stability Element glyph was previously also associated with SO:0001957, but that SO term hasbeen declared obsolete in Sequence Ontology.

This glyph is not backwards compatible with SBOL Visual 1.0.

Despite both being stem-top glyphs, Biopolymer Location is not a parent to Stability Element,since the length of a Stability Element is typically multiple bases / amino acids.


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Sticky End Restriction Enzyme Cleavage Site


SO:0001975 (5' Sticky Restriction Site)

SO:0001976 (3' Sticky Restriction Site)


The 5' sticky restriction site glyph is an image of the lines along which two strands of DNA will becut into 5' sticky ends, and the complementary 3' Sticky Restriction Site glyph is a reflection of the5' Sticky Restriction Site. Vertical position with respect to the backbone is in a break in a singlebackbone (in order: five-prime, three-prime):

and between strands of a double backbone (in order: five-prime double stranded, three-primedouble stranded):



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EcoRI restriction site.

Notes


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Stop Site (Transcrition/Translation End Point)


SO:0000616 Transcription End Site

SO:0000319 Stop Codon;SO:0000327 Coding End, Translation Termination Site, Translation End


Transcription/Translation End Point is a "stem-top" glyph for describing small sites. In thissystem:

the top glyph indicates the type of site (e.g., Biopolymer Location)the stem glyph indicates whether the site affects DNA, RNA, or protein (respectively:straight, wavy, or looped)

The Transcription/Translation End Point top is an asterisk in a circle (in order: transcription,translation):



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Location where a terminator causes transcription to stop, stop codon

Notes

Note that the number of points in the asterisk is not specified, accomodating font differences.


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Terminator


SO:0000141: Terminator


The terminator is a T sitting atop the backbone:


T1 terminator

Notes



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Unspecified


Unspecified: SO:0000110 Sequence Feature


Unspecified is represented by the unicode "replacement character" glyph, indicating a missing orinvalid symbol, is RECOMMENDED:

A half-rounded rectangle, the SBGN glyph for a nucleic acid, is an alternative:


An anonymous sequence that is missing any information about its nature or intended purpose.

Notes

The Unspecified glyph is intended for showing where a sequence's role is missing (or, equivalently,given only the uninformative "Sequence Feature" root role). It should never appear with well-curated designs or diagrams.


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A.2 Molecular Species Glyphs 1

These glyphs represent molecular species in a diagram, and include a bounding box (grey dashed box) but are not 2

connected to any nucleic acid backbone. 3


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Complex

Associated SBO term(s)

SBO:0000253 Non-covalent complex


The RECOMMENDED glyph for a complex is a composite of the glyphs for the molecules ofcomprising the complex. For example, a protein bound to a simple chemical, a protein bound to aguide RNA, or two proteins bound together:

An alternative is the SBGN "cornered rectangle" glyph for a complex:


Arabinose bound to AraC

Notes

Alternate BioPAX definition: Complex: http://www.biopax.org/release/biopax-level3.owl#Complex


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Double-Stranded Nucleic Acid


SBO:0000251 Deoxyribonucleic acid


The RECOMMENDED glyph for dsNA is a double-helix:

An alternative is the SBGN "nucleic acid" half-round rectangle:


DNA fragment during assembly

Notes

Alternate BioPAX definition: Dna: http://www.biopax.org/release/biopax-level3.owl#Dna


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Macromolecule


SBO:0000245 Macromolecule


The macromolecule glyph is a rounded rectangle, as used in SBGN:

A deprecated alternative is a diagonally offset union of a large and small circle, intended to invokethe complex shapes of protein. It is now deprecated for being too similar to a yeast cell "shmoo"symbol:


AraC protein, polymerized chitin

Notes



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No Glyph Assigned


Any SBO type that is not covered by any glyph besides the root


When a species has no assigned glyph it is RECOMMENDED that a user provide their own glyph.The user is also encouraged to submit the new glyph for possible adoption into the SBOLvstandard.

An alternative option is to have a bracket, suggesting information that needs to be filled in:


No Glyph Assigned is intended to be used for any chemical species whose type is not covered byother SBOL Visual glyphs.

Notes

No Glyph Assigned is intended for molecular species with a defined specific type that happens tonot yet be covered by available approved glyphs (other than the root). It is more likely to appear inmachine-generated diagrams than in human-generated diagrams, since humans are likely toinvent and use their own glyph for the purpose.


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Protein


SBO:0000252 Polypeptide Chain


The protein glyph is a "pill" shape with a rectangular body and rounded ends, representing thecompact space-filling mass of many proteins:


AraC protein

Notes

To avoid confusion with circles or ellipses, the "pill" shape SHOULD be significantly longer than itis tall, emphasizing its straight sides.

Alternate BioPAX definition: Protein: http://www.biopax.org/release/biopax-level3.owl#Protein


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Simple Chemical


SBO:0000247 Simple chemical


The simple chemical glyph is any one of three small polygonal shapes, triangle, pentagon, orhexagon:

Alternately, a simple chemical may also be represented a small circle:


Arabinose

Notes

It is RECOMMENDED that visual differentiation be maximized by associating each distinct speciesin a diagram with a different small geometric shape. Rotations may also be used (e.g., pentagonpointing up vs. pentagon pointing down).

It is RECOMMENDED that labels should be placed outside of the shapes rather than inside, to avoidsqueezing the labels.

To avoid confusion with pills or ellipses, when the small circle alternative glyph is used, it SHOULDbe significantly smaller than other types of molecular species glyphs, as indicated by therecommended scale of the glyph.

Alternate BioPAX definition: Small Molecule: http://www.biopax.org/release/biopax-level3.owl#SmallMolecule


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Single-Stranded Nucleic Acid


SBO:0000250 Ribonucleic acid


The RECOMMENDED glyph for ssNA is a wiggly line:

An alternative is the SBGN "nucleic acid" half-round rectangle:


mRNA, gRNA, siRNA

Notes

Alternate BioPAX definition: Rna: http://www.biopax.org/release/biopax-level3.owl#Rna


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Unspecified


SBO:0000285 Material entity of unspecified nature


Unspecified is RECOMMENDED to be represented by the unicode "replacement character" glyph,indicating a missing or invalid symbol:

An alternative is the SBGN "generic species" glyph, which is an ellipse:


An anonymous chemical species that is missing any information about its nature or intendedpurpose.

Notes

The Unspecified glyph is intended for showing where a chemical species' type is missing (or,equivalently, given only the uninformative root role). It should never appear with well-curateddesigns or diagrams.

Alternate BioPAX definition: PhysicalEntity: http://www.biopax.org/release/biopax-level3.owl#PhysicalEntity


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A.3 Interaction Glyphs 1

These glyphs are different forms of “arrow” representing interactions between sequence features and/or molecular 2

species. As arrows, they are extensible and do not have a separately identified bounding box. 3


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Control


SBO:0000168 Control

Head: SBO:0000644 Modified

Tail: SBO:0000019 Modifier


An arrow with a diamond head:


Inversion of a sequence flanked by FRT sites by FLP recombinase

Notes

This section left intentionally blank


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Degradation


SBO:0000179 Degradation

Head: n/a

Tail: SBO:0000010 Reactant


Identical to the Process glyph, but with an empty set at the sink of the arrowhead:


Cellular recycling of mRNA

Notes



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Inhibition


SBO:0000169 Inhibition

Head: SBO:0000642 Inhibited

Tail: SBO:0000020 Inhibitor


An arrow whose head is a bar, suggesting blocking:


Repression of pTAL14 promoter by TAL14

Notes



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Process


SBO:0000375 Process

Head: SBO:0000011 Product

Tail: SBO:0000010 Reactant, SBO:0000645 Template (Genetic Production only)


An arrow with a filled head the same color as the line:


Production of Green Fluorescent Protein (GFP) from the gfp Coding Sequence

Notes

The assocated SBO term also covers:

SBO:0000176 Biochemical ReactionSBO:0000589 Genetic Production (source is DNAcomponent, sink is usually RNA orMacromolecule)SBO:0000177 Non-covalent Binding (sink is a Complex)


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Stimulation


SBO:0000170 Stimulation

Head: SBO:0000643 Stimulated

Tail: SBO:0000459 Stimulator


An arrow with an head that is empty or of a different color than the line:


Activation of pTAL14 promoter by Gal4VP16 activator

Notes



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2.1.0

A.4 Interaction Node Glyphs 1

These glyphs are placed at the junctions of edges to represent biochemical processes, and include a bounding box 2

(grey dashed box) but are not connected to any nucleic acid backbone. Grey dashed lines provide examples of how 3

edges may connect to the glyph. 4


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Association


SBO:0000177 Non-Covalent Binding

Incoming: SBO:0000010 Reactant

Outgoing: SBO:0000011 Product


A circular node:


Association of gRNA and Cas9 to form an active CRISPR complex.

Notes

The association glyph is based on the SBGN Process Description association glyph.


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Dissociation


SBO:0000180 Dissociation




An circular node inside another circle


Dissociation of an active CRISPR complex into gRNA and Cas9.

Notes

The dissociation glyph is based on the SBGN Process Description dissociation glyph.


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Process


SBO:0000375 Process




A square node:


Association of gRNA and Cas9 to form an active CRISPR complex.

Notes

The process glyph is based on the SBGN Process Description process glyph.

The assocated SBO term also covers:

SBO:0000176 Biochemical ReactionSBO:0000177 Non-covalent Binding (sink is a Complex)


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B Examples 1

This section contains prototypical examples, including use of all current glyphs to attempt to ensure that their use is 2

clear. 3

gfppTet

Figure 24: DNA sequence for a functional unit in which the pTet promoter and an anonymous ribosome entry site regulateexpression of a coding sequence for GFP, ended by a terminator.

gfppTet

Figure 25: The same functional unit as in Figure 24, with additional assembly-focused information: there is a 5’ overhangbefore the promoter, a 3’ overhand after the terminator, and an assembly scar between the promoter and the ribosomeentry site left over from a prior step of assembly.

pTet

Figure 26: Promoter pTet stored in a circular plasmid. The promoter is prepared for being cut out of the plasmid: it ispreceded by a 5’ sticky end restriction site and followed by a 3’ stick end restriction site. In addition, the plasmid has beenbar-coded with a signature and has its origin of replication marked.

pTet%

Figure 27: Promoter stored in a plasmid as in Figure 26, except that the restriction sites before and after the promoter areblunt-end.

2.1.0


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Section B. Examples

pTet

Figure 28: Promoter stored in a plasmid as in Figure 26, except that the cut structure of the restriction sites before andafter the promoter is not specified.

pTet

Figure 29: Promoter stored in a plasmid as in Figure 26, except that there is a ribonuclease site after the promoter ratherthan restriction sites flanking it.

Figure 30: Detailed design of a promoter, in which the transcription start site is preceded by two operator sites whereregulators bind, and the whole is flanked by insulators.

pTet

… gfp

Figure 31: Promoter regulating the production of an engineered composite sequence that includes RNA and proteinstability elements at its 3’ end, as well as an internal site for protease cleavage, as well as the expansion of the compositeto show it contains a ribosome entry site. coding sequence, and other omitted details. Single residue locations of interestare indicated for the DNA (before the promoter), RNA (after the ribosome entry site), and protein (in the CDS).

Figure 32: DNA sequence with three primer binding sites.

pTet

?

Figure 33: The same functional unit as in Figure 24, except that information about the CDS is missing, leaving it to fallback on the default unspecified glyph.


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Section B. Examples

AAAgfp

Flp

Figure 34: Promoter regulating the expression of GFP, which is also regulated by an aptamer between it and the poly-A tailof the transcript. The promoter can be cut out by a pair of recombinase target sites, which are acted on by the Flp protein.The whole construct is stored in a circular plasmid with an origin of replication and also an origin of transfer.

Figure 35: Promoter stimulated by the CDS that it regulates.

tetrJ23101

gfppTet

�?�

GFP

Figure 36: Constitutive production of TetR, except that information about the protein is missing, leaving it as the defaultunspecified glyph. TetR represses the pTet promoter, which is regulating production of GFP. The diagram of GFP productionexplicitly includes the intermediate mRNA and the degradation of both the mRNA and protein products.

Figure 37: Phosphorylation of an inactive transcription factor (produced by two different CDSs) by a kinase to form anactive transcriptional activator, which then stimulates a promoter.


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C Relationship to SBOL Visual 1.0 1

SBOL Visual 2.0 differs from SBOL Visual 1.0 in the following major ways: 2

■ Diagram syntax is expanded to include functional interactions and other molecular species. 3

■ The relationship between diagrams and the SBOL data model is made explicit. 4

■ A number of requirements and best practices are specified for glyphs and diagrams, including: 5

• Glyphs include information on interior, bounding box, and recommended backbone alignment. 6

• Sequence feature glyphs are required to have their bounding boxes contact the nucleic acid backbone. 7

• Nucleic acid diagrams now require the nucleic acid backbone line, and the number of lines allowed in 8

various circumstances is constrained. 9

• Explicit statement of when a glyph can and cannot be used to represent a particular element of a 10

diagram. 11

■ Labels that name objects are distinguished from other types of textual annotation. 12

■ Explicit statement of which aspects of a symbol are not controlled. 13

■ Symbol variants are now supported. 14

In addition, the collection of sequence feature glyphs have been expanded and modified in the following ways: 15

■ All non-ambiguous glyphs have been provided with bounding box, interior, and recommended backbone 16

alignment. 17

■ The User Defined glyph has been split into Unspecified, No Glyph Assigned, Engineered Region, and Compos- 18

ite. 19

■ Glyphs have been added for Aptamer, Omitted Detail, Biopolymer Location, Non-Coding RNA Gene, Origin of 20

Transfer, PolyA Site, and Specific Recombination Site. 21

■ The following ontology terms have been assigned or adjusted: 22

• Ribonuclease Site has been assigned SO:0001977. 23

• 5’ Sticky End Restriction Site has been assigned SO:0001975. 24

• 3’ Sticky End Restriction Site has been assigned SO:0001976. 25

• Signature has been assigned SO:0001978. 26

• RNA Stability Element has been updated from the obsolete SO:0001957 to the current SO:0001979 27

• Restriction Enzyme Recognition Site, in addition to SO:0000139 has a second definition as SO:0000061. 28

• 5’ Overhang Site and 3’ Overhang Site were erroneously listed with their ontology terms exchanged; this 29

has been fixed. 30


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References 1

Courtot, M., Juty, N., Knüpfer, C., Waltemath, D., Zhukova, A., Dräger, A., Dumontier, M., Finney, A., Golebiewski, 2

M., Hastings, J., et al. (2011). Controlled vocabularies and semantics in systems biology. Molecular systems biology, 3

7(1):543. 4

Eilbeck, K., Lewis, S. E., Mungall, C. J., Yandell, M., Stein, L., Durbin, R., and Ashburner, M. (2005). The Sequence 5

Ontology: a tool for the unification of genome annotations. Genome biology, 6(5):R44. 6

Le Novère, N., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I., 7

Wimalaratne, S. M., Bergman, F. T., Gauges, R., Ghazal, P., Kawaji, H., Li, L., Matsuoka, Y., Villéger, A., Boyd, S. E., 8

Calzone, L., Courtot, M., Dogrusoz, U., Freeman, T. C., Funahashi, A., Ghosh, S., Jouraku, A., Kim, S., Kolpakov, F., 9

Luna, A., Sahle, S., Schmidt, E., Watterson, S., Wu, G., Goryanin, I., Kell, D. B., Sander, C., Sauro, H., Snoep, J. L., 10

Kohn, K., and Kitano, H. (2009). The systems biology graphical notation. Nat. Biotechnol., 27(8):735–741. 11


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synthetic biology open language visual (sbol visual) version 2(p. fontanarrosa) vishwesh kulkarni:...

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